The office of President Maithripala Sirisena said in a statement Saturday evening that National Thawheed Jammath, or NTJ, and Jamathei Millathu Ibraheem, or JMI, would be banned by presidential decree.
Presidential spokesman Dharmasri Ekanayake says the move allows the government to confiscate any property belonging to the two organizations.
On Monday, officials confirmed that the alleged leader of the Muslim extremist group, an offshoot of NTJ, had died in one of the coordinated suicide bombings at churches and hotels that killed more than 250 people.
A girl and a woman have survived a fiery explosion at a suspected militant safe house in eastern Sri Lanka that killed 15 people during a raid linked to the Easter bombings.
Police spokesman Ruwan Gunasekara said Saturday that the woman and girl are critically injured and are being treated at a nearby hospital in Ampara District.
Sri Lankan security forces have been clearing the safe house following a Friday night gunbattle between soldiers and suspected militants. Authorities say the militants set off three explosions and opened fire.
Police say they found 15 bodies including six children at the house.
Pictures by The Associated Press show the charred remains of one child. The body of another child can be seen in a green T-shirt with the words "good boy" written on the back.
The bodies of an adult woman and man were found after the explosion with their clothes burned off.
Police say that 15 bodies including six children have been found after a raid in east Sri Lanka on militants linked to the Easter bombings.
Police spokesman Ruwan Gunasekara gave the figures early Saturday after a gunfight between soldiers and the suspected militants near Sammanthurai.
The gunbattle began Friday night after police tipped off soldiers to a suspected safe house, where authorities say the militants set off three explosions and opened fire. At least three others were wounded in the attack.
Gunasekara says some of the dead likely were militants who blew themselves up in suicide bombings.
Earlier, the military said at least one civilian had been killed in the attack.
Sri Lanka's military says soldiers are raiding an area in the country's east where a gunfight between troops and suspects linked to the Easter suicide bombings killed two militants and one civilian.
Maj. Gen. Aruna Jayasekara, the local military commander, said Saturday that at least three people were wounded in the gunbattle that saw at least three explosions.
Jayasekara says soldiers and police wanted to wait until daylight to carry out further raids given houses being built so close together.
Meanwhile, the military says security forces have recovered explosives, detonators, "suicide kits," military uniforms and Islamic State group flags during the raids.
The Easter suicide bombings, claimed by the Islamic State group, targeted churches and hotels and killed at least 250 people.